[Cdk-devel] [ cdk-Patches-3154364 ] CTFile query bonds

Patches item #3154364, was opened at 2011-01-10 15:35
Message generated for change (Settings changed) made by mark_rynbeek
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Category: master
Group: Needs Review
Status: Open
Resolution: None
Priority: 5
Private: No
Submitted By: Mark Rijnbeek (mark_rynbeek)
>Assigned to: Rajarshi Guha (rajarshi)
Summary: CTFile query bonds
Initial Comment:
Problem: the current MDL reader trips over bond types 5,6,7,8 as defined in the CTFile:
5 = Single or Double
6 = Single or Aromatic
7 = Double or Aromatic
8 = Any
Egon and me made patches to deal with this. It's a bit extensive, because as part of the patch the link between modules 'isomorphism' and 'data' is broken. Otherwise, the main idea of the patch is that the MDL reader now, when encountering a query bond type, creates a QueryAtomContainer instead of a regular Molecule. The query bonds are CTFileQueryBond objects for which the types 5..8 above can be set.
----------------------------------------------------------------------
You can respond by visiting:
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Patches item #3154364, was opened at 2011-01-10 15:35
Message generated for change (Tracker Item Submitted) made by mark_rynbeek
You can respond by visiting:
https://sourceforge.net/tracker/?func=detail&atid=320024&aid=3154364&group_id=20024
Please note that this message will contain a full copy of the comment thread,
including the initial issue submission, for this request,
not just the latest update.
Category: master
Group: Needs Review
Status: Open
Resolution: None
Priority: 5
Private: No
Submitted By: Mark Rijnbeek (mark_rynbeek)
Assigned to: Nobody/Anonymous (nobody)
Summary: CTFile query bonds
Initial Comment:
Problem: the current MDL reader trips over bond types 5,6,7,8 as defined in the CTFile:
5 = Single or Double
6 = Single or Aromatic
7 = Double or Aromatic
8 = Any
Egon and me made patches to deal with this. It's a bit extensive, because as part of the patch the link between modules 'isomorphism' and 'data' is broken. Otherwise, the main idea of the patch is that the MDL reader now, when encountering a query bond type, creates a QueryAtomContainer instead of a regular Molecule. The query bonds are CTFileQueryBond objects for which the types 5..8 above can be set.
----------------------------------------------------------------------
You can respond by visiting:
https://sourceforge.net/tracker/?func=detail&atid=320024&aid=3154364&group_id=20024

Patches item #3154364, was opened at 2011-01-10 15:35
Message generated for change (Settings changed) made by mark_rynbeek
You can respond by visiting:
https://sourceforge.net/tracker/?func=detail&atid=320024&aid=3154364&group_id=20024
Please note that this message will contain a full copy of the comment thread,
including the initial issue submission, for this request,
not just the latest update.
Category: master
Group: Needs Review
Status: Open
Resolution: None
Priority: 5
Private: No
Submitted By: Mark Rijnbeek (mark_rynbeek)
>Assigned to: Rajarshi Guha (rajarshi)
Summary: CTFile query bonds
Initial Comment:
Problem: the current MDL reader trips over bond types 5,6,7,8 as defined in the CTFile:
5 = Single or Double
6 = Single or Aromatic
7 = Double or Aromatic
8 = Any
Egon and me made patches to deal with this. It's a bit extensive, because as part of the patch the link between modules 'isomorphism' and 'data' is broken. Otherwise, the main idea of the patch is that the MDL reader now, when encountering a query bond type, creates a QueryAtomContainer instead of a regular Molecule. The query bonds are CTFileQueryBond objects for which the types 5..8 above can be set.
----------------------------------------------------------------------
You can respond by visiting:
https://sourceforge.net/tracker/?func=detail&atid=320024&aid=3154364&group_id=20024

Patches item #3154364, was opened at 2011-01-10 10:35
Message generated for change (Comment added) made by rajarshi
You can respond by visiting:
https://sourceforge.net/tracker/?func=detail&atid=320024&aid=3154364&group_id=20024
Please note that this message will contain a full copy of the comment thread,
including the initial issue submission, for this request,
not just the latest update.
Category: master
Group: Needs Review
Status: Open
Resolution: None
Priority: 5
Private: No
Submitted By: Mark Rijnbeek (mark_rynbeek)
Assigned to: Rajarshi Guha (rajarshi)
Summary: CTFile query bonds
Initial Comment:
Problem: the current MDL reader trips over bond types 5,6,7,8 as defined in the CTFile:
5 = Single or Double
6 = Single or Aromatic
7 = Double or Aromatic
8 = Any
Egon and me made patches to deal with this. It's a bit extensive, because as part of the patch the link between modules 'isomorphism' and 'data' is broken. Otherwise, the main idea of the patch is that the MDL reader now, when encountering a query bond type, creates a QueryAtomContainer instead of a regular Molecule. The query bonds are CTFileQueryBond objects for which the types 5..8 above can be set.
----------------------------------------------------------------------
>Comment By: Rajarshi Guha (rajarshi)
Date: 2011-01-17 12:09
Message:
I think it looks OK - quite a big patch!
But 0005-QueryAtomContainer-to-allowe-atoms-and-bonds.patch fails to
apply
----------------------------------------------------------------------
You can respond by visiting:
https://sourceforge.net/tracker/?func=detail&atid=320024&aid=3154364&group_id=20024

Patches item #3154364, was opened at 2011-01-10 16:35
Message generated for change (Comment added) made by egonw
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Please note that this message will contain a full copy of the comment thread,
including the initial issue submission, for this request,
not just the latest update.
Category: master
Group: Needs Review
Status: Open
Resolution: None
Priority: 5
Private: No
Submitted By: Mark Rijnbeek (mark_rynbeek)
Assigned to: Rajarshi Guha (rajarshi)
Summary: CTFile query bonds
Initial Comment:
Problem: the current MDL reader trips over bond types 5,6,7,8 as defined in the CTFile:
5 = Single or Double
6 = Single or Aromatic
7 = Double or Aromatic
8 = Any
Egon and me made patches to deal with this. It's a bit extensive, because as part of the patch the link between modules 'isomorphism' and 'data' is broken. Otherwise, the main idea of the patch is that the MDL reader now, when encountering a query bond type, creates a QueryAtomContainer instead of a regular Molecule. The query bonds are CTFileQueryBond objects for which the types 5..8 above can be set.
----------------------------------------------------------------------
>Comment By: Egon Willighagen (egonw)
Date: 2011-02-13 17:09
Message:
Rajarshi, there is a mix set of patches.... two 0001 patches, etc... I'll
try if I can remove the dups...
----------------------------------------------------------------------
Comment By: Rajarshi Guha (rajarshi)
Date: 2011-01-17 18:09
Message:
I think it looks OK - quite a big patch!
But 0005-QueryAtomContainer-to-allowe-atoms-and-bonds.patch fails to
apply
----------------------------------------------------------------------
You can respond by visiting:
https://sourceforge.net/tracker/?func=detail&atid=320024&aid=3154364&group_id=20024

Patches item #3154364, was opened at 2011-01-10 16:35
Message generated for change (Comment added) made by egonw
You can respond by visiting:
https://sourceforge.net/tracker/?func=detail&atid=320024&aid=3154364&group_id=20024
Please note that this message will contain a full copy of the comment thread,
including the initial issue submission, for this request,
not just the latest update.
Category: master
Group: Needs Review
Status: Open
Resolution: None
Priority: 5
Private: No
Submitted By: Mark Rijnbeek (mark_rynbeek)
Assigned to: Rajarshi Guha (rajarshi)
Summary: CTFile query bonds
Initial Comment:
Problem: the current MDL reader trips over bond types 5,6,7,8 as defined in the CTFile:
5 = Single or Double
6 = Single or Aromatic
7 = Double or Aromatic
8 = Any
Egon and me made patches to deal with this. It's a bit extensive, because as part of the patch the link between modules 'isomorphism' and 'data' is broken. Otherwise, the main idea of the patch is that the MDL reader now, when encountering a query bond type, creates a QueryAtomContainer instead of a regular Molecule. The query bonds are CTFileQueryBond objects for which the types 5..8 above can be set.
----------------------------------------------------------------------
>Comment By: Egon Willighagen (egonw)
Date: 2011-02-13 17:16
Message:
Rajarshi, please try the new tar.gz.
----------------------------------------------------------------------
Comment By: Egon Willighagen (egonw)
Date: 2011-02-13 17:09
Message:
Rajarshi, there is a mix set of patches.... two 0001 patches, etc... I'll
try if I can remove the dups...
----------------------------------------------------------------------
Comment By: Rajarshi Guha (rajarshi)
Date: 2011-01-17 18:09
Message:
I think it looks OK - quite a big patch!
But 0005-QueryAtomContainer-to-allowe-atoms-and-bonds.patch fails to
apply
----------------------------------------------------------------------
You can respond by visiting:
https://sourceforge.net/tracker/?func=detail&atid=320024&aid=3154364&group_id=20024

Patches item #3154364, was opened at 2011-01-10 10:35
Message generated for change (Comment added) made by rajarshi
You can respond by visiting:
https://sourceforge.net/tracker/?func=detail&atid=320024&aid=3154364&group_id=20024
Please note that this message will contain a full copy of the comment thread,
including the initial issue submission, for this request,
not just the latest update.
Category: master
Group: Needs Review
Status: Open
Resolution: None
Priority: 5
Private: No
Submitted By: Mark Rijnbeek (mark_rynbeek)
Assigned to: Rajarshi Guha (rajarshi)
Summary: CTFile query bonds
Initial Comment:
Problem: the current MDL reader trips over bond types 5,6,7,8 as defined in the CTFile:
5 = Single or Double
6 = Single or Aromatic
7 = Double or Aromatic
8 = Any
Egon and me made patches to deal with this. It's a bit extensive, because as part of the patch the link between modules 'isomorphism' and 'data' is broken. Otherwise, the main idea of the patch is that the MDL reader now, when encountering a query bond type, creates a QueryAtomContainer instead of a regular Molecule. The query bonds are CTFileQueryBond objects for which the types 5..8 above can be set.
----------------------------------------------------------------------
Comment By: Rajarshi Guha (rajarshi)
Date: 2011-02-13 11:19
Message:
there are still two 0001-* patches
----------------------------------------------------------------------
Comment By: Egon Willighagen (egonw)
Date: 2011-02-13 11:16
Message:
Rajarshi, please try the new tar.gz.
----------------------------------------------------------------------
Comment By: Egon Willighagen (egonw)
Date: 2011-02-13 11:09
Message:
Rajarshi, there is a mix set of patches.... two 0001 patches, etc... I'll
try if I can remove the dups...
----------------------------------------------------------------------
Comment By: Rajarshi Guha (rajarshi)
Date: 2011-01-17 12:09
Message:
I think it looks OK - quite a big patch!
But 0005-QueryAtomContainer-to-allowe-atoms-and-bonds.patch fails to
apply
----------------------------------------------------------------------
You can respond by visiting:
https://sourceforge.net/tracker/?func=detail&atid=320024&aid=3154364&group_id=20024

Patches item #3154364, was opened at 2011-01-10 10:35
Message generated for change (Comment added) made by rajarshi
You can respond by visiting:
https://sourceforge.net/tracker/?func=detail&atid=320024&aid=3154364&group_id=20024
Please note that this message will contain a full copy of the comment thread,
including the initial issue submission, for this request,
not just the latest update.
Category: master
Group: Needs Review
Status: Open
Resolution: None
Priority: 5
Private: No
Submitted By: Mark Rijnbeek (mark_rynbeek)
Assigned to: Rajarshi Guha (rajarshi)
Summary: CTFile query bonds
Initial Comment:
Problem: the current MDL reader trips over bond types 5,6,7,8 as defined in the CTFile:
5 = Single or Double
6 = Single or Aromatic
7 = Double or Aromatic
8 = Any
Egon and me made patches to deal with this. It's a bit extensive, because as part of the patch the link between modules 'isomorphism' and 'data' is broken. Otherwise, the main idea of the patch is that the MDL reader now, when encountering a query bond type, creates a QueryAtomContainer instead of a regular Molecule. The query bonds are CTFileQueryBond objects for which the types 5..8 above can be set.
----------------------------------------------------------------------
>Comment By: Rajarshi Guha (rajarshi)
Date: 2011-02-13 11:21
Message:
Sorry, used the wrong file
----------------------------------------------------------------------
Comment By: Rajarshi Guha (rajarshi)
Date: 2011-02-13 11:19
Message:
there are still two 0001-* patches
----------------------------------------------------------------------
Comment By: Egon Willighagen (egonw)
Date: 2011-02-13 11:16
Message:
Rajarshi, please try the new tar.gz.
----------------------------------------------------------------------
Comment By: Egon Willighagen (egonw)
Date: 2011-02-13 11:09
Message:
Rajarshi, there is a mix set of patches.... two 0001 patches, etc... I'll
try if I can remove the dups...
----------------------------------------------------------------------
Comment By: Rajarshi Guha (rajarshi)
Date: 2011-01-17 12:09
Message:
I think it looks OK - quite a big patch!
But 0005-QueryAtomContainer-to-allowe-atoms-and-bonds.patch fails to
apply
----------------------------------------------------------------------
You can respond by visiting:
https://sourceforge.net/tracker/?func=detail&atid=320024&aid=3154364&group_id=20024